/research-pipeline

name: research-pipeline
description: "Full end-to-end research pipeline: from a broad research direction through idea discovery, experiments, and review all the way to a polished paper PDF. Use when user says \"全流程\", \"full pipeline\", \"从找idea到投稿\", \"end-to-end research\", or wants the complete autonomous research lifecycle."
argument-hint: "[research-direction] [— resume <run_id>]"
allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, WebSearch, WebFetch, Skill, mcp__codex__codex, mcp__codex__codex-reply

Full Research Pipeline: Idea → Experiments → Submission

> ⏱ **External cadence: non-judgmental heartbeat only.** An overnight `/loop` / > `CronCreate` heartbeat may wake, detect a **stalled** phase (no progress, dead > process, blocked on a freed resource) and **nudge** it forward — it may NEVER > decide the work is good (paper good enough, proof holds, claim supported). > Every such verdict stays on its own skill's internal cadence and terminates in > the cross-model jury. A heartbeat may say "keep going," never "good enough." > See > [`shared-references/external-cadence.md`](../shared-references/external-cadence.md) > (overnight-pipeline rule + stall detection & forced structural pivot). At heartbeat > startup, touch the run state first each tick and register this run with the watchdog > `loop` type (so a silent death surfaces as STALE); unregister on completion. The > watchdog only detects — it never acquits. Each tick also record the new-finding count > via the `iteration_log.py` helper (resolve through the canonical > `.aris/tools → tools → $ARIS_REPO/tools → $ARIS_REPO/tools via ~/.aris/repo` > chain, integration-contract §2; warn-and-skip if unresolved): > `python3 "$ITER_LOG" note <root> <run_id> <phase> <n>`. On the returned > `pivot=structural` (stale ≥ 2) the nudge must change a STRUCTURAL constraint and pick an > untried direction; on `pivot=human` (stale ≥ 4) flag for attention. Counting only — > never a quality verdict.

End-to-end autonomous research workflow for: **$ARGUMENTS**

Constants

• **AUTO_PROCEED = true** — When `true`, every selection checkpoint is informational: report the choice and continue in the same turn. When `false`, ask for explicit user confirmation and end the turn at the checkpoint.
• **ARXIV_DOWNLOAD = false** — When `true`, `/research-lit` downloads the top relevant arXiv PDFs during literature survey. When `false` (default), only fetches metadata via arXiv API. Passed through to `/idea-discovery` → `/research-lit`.
• **HUMAN_CHECKPOINT = false** — When `true`, the auto-review loops (Stage 3) pause after each round's review to let you see the score and provide custom modification instructions before fixes are implemented. When `false` (default), loops run fully autonomously. Passed through to `/auto-review-loop`.
• **REVIEWER_DIFFICULTY = medium** — How adversarial the reviewer is. `medium` (default): standard MCP review. `hard`: adds reviewer memory + debate protocol. `nightmare`: GPT reads repo directly via `codex exec` + memory + debate. Passed through to `/auto-review-loop`.
• **CODE_REVIEW = true** — GPT-6-Astra xhigh reviews experiment code before deployment. Catches logic bugs before wasting GPU hours. Set `false` to skip. Passed through to `/experiment-bridge`.
• **BASE_REPO = false** — GitHub repo URL to use as base codebase. When set, `/experiment-bridge` clones the repo first and implements experiments on top of it. When `false` (default), writes code from scratch or reuses existing project files. Passed through to `/experiment-bridge`.
• **COMPACT = false** — When `true`, generates compact summary files for short-context models and session recovery. Passed through to `/idea-discovery` and `/experiment-bridge`.
• **AUTO_WRITE = false** — When `true`, automatically invoke Workflow 3 (`/paper-writing`) after Stage 4. `VENUE` is needed only when Stage 5 begins — a missing venue defers paper writing; it never blocks Stages 1-4. When `false` (default), Stage 4 generates `NARRATIVE_REPORT.md` and stops — user invokes `/paper-writing` manually.
• **VENUE = (unset)** — Target venue for paper writing; bound only when Stage 5 begins. Options: `ICLR`, `NeurIPS`, `ICML`, `CVPR`, `ACL`, `AAAI`, `ACM`, `IEEE_CONF`, `IEEE_JOURNAL`. No default: a missing venue defers paper writing — it never blocks Stages 1-4 and is never guessed.
• **RENDER_HTML = true** — When `true` (default), auto-render `NARRATIVE_REPORT.md` to HTML at Stage 4 completion via `/render-html`. Uses `--no-review` (this is an internal handoff doc to `/paper-writing`, not a reviewer-facing final artifact — the upstream Stage 3 auto-review loop already cross-model-reviewed the claims). Set `false` to skip, or pass `— render html: false`. **Non-blocking**: if `/render-html` fails or Codex MCP is unavailable, log the failure and continue — the HTML view is a nice-to-have, not a Stage 4 prerequisite.

• **RESUMABLE = true** — When `true` (default), the pipeline records per-stage state to `.aris/runs/<run_id>.json` so a crashed/interrupted run can resume via `/research-pipeline — resume <run_id>` instead of restarting. Stage status splits `done` (executor finished writing) from `accepted` (the stage's cross-model gate / deterministic verifier passed); resume re-validates any `done`-but-unaccepted stage. See `shared-references/resumable-runs.md`.

> 💡 Override via argument, e.g., `/research-pipeline "topic" — AUTO_PROCEED: false, human checkpoint: true, difficulty: nightmare, code review: false, base repo: https://github.com/org/project, auto_write: true, venue: NeurIPS`.

Checkpoint execution rule

Resolve `AUTO_PROCEED` once from `$ARGUMENTS` before Stage 1 and pass that resolved value to nested workflows.

• **`AUTO_PROCEED=true` is non-blocking.** A checkpoint is a progress update,

not a question. State the result and the automatically selected next action, then continue executing in the **same turn**. Do not ask for confirmation, request user input, sleep, w